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Samach A, Mafessoni F, Gross O, Melamed-Bessudo C, Filler-Hayut S, Dahan-Meir T, Amsellem Z, Pawlowski WP, Levy AA. CRISPR/Cas9-induced DNA breaks trigger crossover, chromosomal loss, and chromothripsis-like rearrangements. THE PLANT CELL 2023; 35:3957-3972. [PMID: 37497643 PMCID: PMC10615209 DOI: 10.1093/plcell/koad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
DNA double-stranded breaks (DSBs) generated by the Cas9 nuclease are commonly repaired via nonhomologous end-joining (NHEJ) or homologous recombination (HR). However, little is known about unrepaired DSBs and the type of damage they trigger in plants. We designed an assay that detects loss of heterozygosity (LOH) in somatic cells, enabling the study of a broad range of DSB-induced genomic events. The system relies on a mapped phenotypic marker which produces a light purple color (betalain pigment) in all plant tissues. Plants with sectors lacking the Betalain marker upon DSB induction between the marker and the centromere were tested for LOH events. Using this assay, we detected a tomato (Solanum lycopersicum) flower with a twin yellow and dark purple sector, corresponding to a germinally transmitted somatic crossover event. We also identified instances of small deletions of genomic regions spanning the T-DNA and whole chromosome loss. In addition, we show that major chromosomal rearrangements including loss of large fragments, inversions, and translocations were clearly associated with the CRISPR-induced DSB. Detailed characterization of complex rearrangements by whole-genome sequencing and molecular and cytological analyses supports a model in which a breakage-fusion-bridge cycle followed by chromothripsis-like rearrangements had been induced. Our LOH assay provides a tool for precise breeding via targeted crossover detection. It also uncovers CRISPR-mediated chromothripsis-like events in plants.
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Affiliation(s)
- Aviva Samach
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Fabrizio Mafessoni
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Or Gross
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Cathy Melamed-Bessudo
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Shdema Filler-Hayut
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Tal Dahan-Meir
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | - Ziva Amsellem
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
| | | | - Avraham A Levy
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot 7610001,Israel
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2
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Nath O, Fletcher SJ, Hayward A, Shaw LM, Agarwal R, Furtado A, Henry RJ, Mitter N. A Comprehensive High-Quality DNA and RNA Extraction Protocol for a Range of Cultivars and Tissue Types of the Woody Crop Avocado. PLANTS 2022; 11:plants11030242. [PMID: 35161230 PMCID: PMC8838124 DOI: 10.3390/plants11030242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/11/2023]
Abstract
High-quality DNA and RNA forms the basis of genomic and genetic investigations. The extraction of DNA and RNA from woody trees, like avocado (Persea americana Mill.), is challenging due to compounds which interact with nucleic acids and influence separation. Previously reported methods of DNA and RNA extraction from avocado have issues of low yield, quality and applicability across different cultivars and tissue types. In the current study, methods have been optimised for high-quality DNA extraction from 40 avocado cultivars and RNA extraction from multiple tissue types, including roots, stem, leaves, flowers and fruits. The method is based on the modification of the cetyltrimethylammonium bromide buffer, centred around the specific optimisation of chemicals, such as sodium dodecyl sulphate, polyvinylpyrrolidone, sodium sulphite, polyethylene glycol and β-mercaptoethanol. The DNA extraction method yielded high-molecular weight DNA from the leaf tissue of 40 avocado cultivars belonging to Mexican, Guatemalan and West Indian avocado horticultural groups. The method was further optimised for RNA extraction from different avocado plant parts, enabling extraction using amounts as low as ~10 mg of starting material. The DNA and RNA extracted was successfully used for long- and short-read sequencing and gene expression analysis. The methods developed may also be applicable to other recalcitrant plant species.
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Investigating Transgene Integration and Organization in Cotton (Gossypium hirsutum L.) Genome. Methods Mol Biol 2018. [PMID: 30543066 DOI: 10.1007/978-1-4939-8952-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In this chapter, we present detailed experimental procedures for investigating integration patterns of transgenes in cotton genome. We use conventional PCR and genomic Southern blot hybridization to characterize integration of T-DNA components and vector backbone fragments. For multiple-copy insertions into the same site (complex loci), transgene/transgene junctions (including canonical and truncated T-DNA and transgene involved vector backbone sequences) are characterized by PCR and sequencing. Inverse PCR and sequencing are used to characterize transgene/cotton genome junctions. Distribution of T-DNA insertion in cotton genome is evaluated by analysis of transgene flanking sequences. The pre-insertion sites can also be cloned and sequenced (based on the flanking sequences) for survey of genomic structure changes brought by transgene integration by comparing a pre-insertion site with corresponding transgene/plant junctions.
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Matoušek J, Kocábek T, Patzak J, Bříza J, Siglová K, Mishra AK, Duraisamy GS, Týcová A, Ono E, Krofta K. The "putative" role of transcription factors from HlWRKY family in the regulation of the final steps of prenylflavonid and bitter acids biosynthesis in hop (Humulus lupulus L.). PLANT MOLECULAR BIOLOGY 2016; 92:263-77. [PMID: 27392499 DOI: 10.1007/s11103-016-0510-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 07/02/2016] [Indexed: 05/20/2023]
Abstract
Lupulin glands localized in female hop (Humulus lupulus L.) cones are valuable source of bitter acids, essential oils and polyphenols. These compounds are used in brewing industry and are important for biomedical applications. In this study we describe the potential effect of transcription factors from WRKY family in the activation of the final steps of lupulin biosynthesis. In particular, lupulin gland-specific transcription factor HlWRKY1 that shows significant similarity to AtWRKY75, has ability to activate the set of promoters driving key genes of xanthohumol and bitter acids biosynthesis such as chalcone synthase H1, valerophenone synthase, prenyltransferase 1, 1L and 2 and O-methyltransferase-1. When combined with co-factor HlWDR1 and silencing suppressor p19, HlWRKY1 is able to enhance transient expression of gus gene driven by Omt1 and Chs_H1 promoters to significant level as compared to 35S promoter of CaMV in Nicotiana. benthamiana. Transformation of hop with dual Agrobacterium vector bearing HlWRKY1/HlWDR1 led to ectopic overexpression of these transgenes and further activation of lupulin-specific genes expression in hop leaves. It was further showed that (1) HlWRKY1 is endowed with promoter autoactivation; (2) It is regulated by post-transcriptional gene silencing (PTGS) mechanism; (3) It is stimulated by kinase co-expression. Since HlWRKY1 promotes expression of lupulin-specific HlMyb3 gene therefore it can constitute a significant component in hop lupulin regulation network. Putative involvement of HlWRKY1 in the regulation of lupulin biosynthesis may suggest the original physiological function of lupulin components in hop as flower and seed protective compounds.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Tomáš Kocábek
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Josef Patzak
- Hop Research Institute, Co. Ltd., Kadaňská 2525, 438 46, Žatec, Czech Republic
| | - Jindřich Bříza
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Kristýna Siglová
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Ganesh Selvaraj Duraisamy
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Anna Týcová
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Eiichiro Ono
- Research Institute, Suntory Global Innovation Center (SIC) Ltd., 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka, 618-8503, Japan
| | - Karel Krofta
- Hop Research Institute, Co. Ltd., Kadaňská 2525, 438 46, Žatec, Czech Republic
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5
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Maessen G. Genomic stability and stability of expression in genetically modified plants. ACTA ACUST UNITED AC 2013. [DOI: 10.1111/plb.1997.46.1.3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Carter JD, Pereira A, Dickerman AW, Veilleux RE. An active ac/ds transposon system for activation tagging in tomato cultivar m82 using clonal propagation. PLANT PHYSIOLOGY 2013; 162:145-56. [PMID: 23569107 PMCID: PMC3641199 DOI: 10.1104/pp.113.213876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Tomato (Solanum lycopersicum) is a model organism for Solanaceae in both molecular and agronomic research. This project utilized Agrobacterium tumefaciens transformation and the transposon-tagging construct Activator (Ac)/Dissociator (Ds)-ATag-Bar_gosGFP to produce activation-tagged and knockout mutants in the processing tomato cultivar M82. The construct carried hygromycin resistance (hyg), green fluorescent protein (GFP), and the transposase (TPase) of maize (Zea mays) Activator major transcript X054214.1 on the stable Ac element, along with a 35S enhancer tetramer and glufosinate herbicide resistance (BAR) on the mobile Ds-ATag element. An in vitro propagation strategy was used to produce a population of 25 T0 plants from a single transformed plant regenerated in tissue culture. A T1 population of 11,000 selfed and cv M82 backcrossed progeny was produced from the functional T0 line. This population was screened using glufosinate herbicide, hygromycin leaf painting, and multiplex polymerase chain reaction (PCR). Insertion sites of transposed Ds-ATag elements were identified through thermal asymmetric interlaced PCR, and resulting product sequences were aligned to the recently published tomato genome. A population of 509 independent, Ds-only transposant lines spanning all 12 tomato chromosomes has been developed. Insertion site analysis demonstrated that more than 80% of these lines harbored Ds insertions conducive to activation tagging. The capacity of the Ds-ATag element to alter transcription was verified by quantitative real-time reverse transcription-PCR in two mutant lines. The transposon-tagged lines have been immortalized in seed stocks and can be accessed through an online database, providing a unique resource for tomato breeding and analysis of gene function in the background of a commercial tomato cultivar.
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Zhang J, Hong Y. Investigating transgene integration and organization in cotton (Gossypium hirsutum L.) genome. Methods Mol Biol 2013; 958:95-107. [PMID: 23143486 DOI: 10.1007/978-1-62703-212-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this chapter, we present detailed experimental procedures for investigating integration patterns of transgenes in cotton genome. We use conventional PCR and genomic Southern blot hybridization to characterize integration of T-DNA components and vector backbone fragments. For multiple copy insertions into the same site (complex loci), transgene/transgene junctions (including canonical and truncated T-DNA and transgene involved vector backbone sequences) are characterized by PCR and sequencing. Inverse PCR (see Note 1) and sequencing is used to characterize transgene/cotton genome junctions. Distribution of T-DNA insertion in cotton genome is evaluated by analysis of transgene flanking sequences. The pre-insertion sites can also be cloned and sequenced (based on the flanking sequences) for survey of genomic structure changes brought by transgene integration by comparing a pre-insertion site with corresponding transgene/plant junctions.
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Affiliation(s)
- Jun Zhang
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, PR China
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8
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El-Kharbotly A, Jacobs JM, Hekkert BT, Stiekema WJ, Pereira A, Jacobsen E, Ramanna MS. Localization of Ds-transposon containing T-DNA inserts in the diploid transgenic potato: linkage to the R1 resistance gene against Phytophthora infestans (Mont.) de Bary. Genome 2012; 39:249-57. [PMID: 18469890 DOI: 10.1139/g96-034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Dissociation transposable element (Ds) of maize containing NPTII was introduced into the diploid potato (Solanum tuberosum) clone J91-6400-A16 through Agrobacterium tumefaciens mediated transformation. Genomic DNA sequences flanking the T-DNAs from 312 transformants were obtained with inverse polymerase chain reaction or plasmid rescue techniques and used as probes for RFLP linkage analysis. The RFLP map location of 60 T-DNAs carrying Ds-NPTII was determined. The T-DNA distribution per chromosome and the relative distance between them appeared to be random. All 12 chromosomes have been covered with Ds-containing T-DNAs, potentially enabling tagging of any gene in the potato genome. The T-DNA insertions of two transformants, BET92-Ds-A16-259 and BET92-Ds-A16-416, were linked in repulsion to the position of the resistance gene R1 against Phytophthora infestans. After crossing BET92-Ds-A16-416 with a susceptible parent, 4 desired recombinants (Ds carrying T-DNA linked in coupling phase with the R1 gene) were discovered. These will be used for tagging the R1 gene. The efficiency of the pathway from the introduction to localization of T-DNAs is discussed. Key words : Solanum tuberosum, Phytophthora infestans, Ds element, transposon tagging, R genes, euchromatin.
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9
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Filipenko EA, Deineko EV, Shumnyi VK. Specific features of T-DNA insertion regions in transgenic plants. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409110040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Saito T, Asamizu E, Mizoguchi T, Fukuda N, Matsukura C, Ezura H. Mutant Resources for the Miniature Tomato ( Solanum lycopersicum L.) ‘Micro-Tom’. ACTA ACUST UNITED AC 2009. [DOI: 10.2503/jjshs1.78.6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takeshi Saito
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Erika Asamizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Tsuyoshi Mizoguchi
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Naoya Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Chiaki Matsukura
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba
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11
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Matsukura C, Aoki K, Fukuda N, Mizoguchi T, Asamizu E, Saito T, Shibata D, Ezura H. Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom. Curr Genomics 2008; 9:436-43. [PMID: 19506732 PMCID: PMC2691670 DOI: 10.2174/138920208786241225] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 07/23/2008] [Accepted: 07/27/2008] [Indexed: 11/22/2022] Open
Abstract
Tomato (Solanum lycopersicum L., Solanaceae) is an excellent model plant for genomic research of solanaceous plants, as well as for studying the development, ripening, and metabolism of fruit. In 2003, the International Solanaceae Project (SOL, www.sgn.cornell.edu ) was initiated by members from more than 30 countries, and the tomato genome-sequencing project is currently underway. Genome sequence of tomato obtained by this project will provide a firm foundation for forthcoming genomic studies such as the comparative analysis of genes conserved among the Solanaceae species and the elucidation of the functions of unknown tomato genes. To exploit the wealth of the genome sequence information, there is an urgent need for novel resources and analytical tools for tomato functional genomics. Here, we present an overview of the development of genetic and genomic resources of tomato in the last decade, with a special focus on the activities of Japan SOL and the National Bio-Resource Project in the development of functional genomic resources of a model cultivar, Micro-Tom.
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Affiliation(s)
- C Matsukura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, 305-8572, Japan
| | - K Aoki
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, 292-0818, Japan
| | - N Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, 305-8572, Japan
| | - T Mizoguchi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, 305-8572, Japan
| | - E Asamizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, 305-8572, Japan
| | - T Saito
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, 305-8572, Japan
| | - D Shibata
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, 292-0818, Japan
| | - H Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, 305-8572, Japan
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Choi J, Park J, Jeon J, Chi MH, Goh J, Yoo SY, Park J, Jung K, Kim H, Park SY, Rho HS, Kim S, Kim BR, Han SS, Kang S, Lee YH. Genome-wide analysis of T-DNA integration into the chromosomes of Magnaporthe oryzae. Mol Microbiol 2007; 66:371-82. [PMID: 17850257 PMCID: PMC2169514 DOI: 10.1111/j.1365-2958.2007.05918.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Agrobacterium tumefaciens-mediated transformation (ATMT) has become a prevalent tool for functional genomics of fungi, but our understanding of T-DNA integration into the fungal genome remains limited relative to that in plants. Using a model plant-pathogenic fungus, Magnaporthe oryzae, here we report the most comprehensive analysis of T-DNA integration events in fungi and the development of an informatics infrastructure, termed a T-DNA analysis platform (TAP). We identified a total of 1110 T-DNA-tagged locations (TTLs) and processed the resulting data via TAP. Analysis of the TTLs showed that T-DNA integration was biased among chromosomes and preferred the promoter region of genes. In addition, irregular patterns of T-DNA integration, such as chromosomal rearrangement and readthrough of plasmid vectors, were also observed, showing that T-DNA integration patterns into the fungal genome are as diverse as those of their plant counterparts. However, overall the observed junction structures between T-DNA borders and flanking genomic DNA sequences revealed that T-DNA integration into the fungal genome was more canonical than those observed in plants. Our results support the potential of ATMT as a tool for functional genomics of fungi and show that the TAP is an effective informatics platform for handling data from large-scale insertional mutagenesis.
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Affiliation(s)
- Jaehyuk Choi
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Jongsun Park
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Junhyun Jeon
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Myoung-Hwan Chi
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Jaeduk Goh
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Sung-Yong Yoo
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Jaejin Park
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Kyongyong Jung
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Hyojeong Kim
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Sook-Young Park
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Hee-Sool Rho
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Soonok Kim
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
| | - Byeong Ryun Kim
- National Institute of Crop Science, Rural Development AdministrationSuwon, 441-857, Korea
| | - Seong-Sook Han
- National Institute of Crop Science, Rural Development AdministrationSuwon, 441-857, Korea
| | - Seogchan Kang
- Department of Plant Pathology, Pennsylvania State University, University ParkPA 16802, USA
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-921, Korea
- E-mail ; Tel. (+82) 2 880 4674; Fax (+82) 2 873 2317
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Thomas CM, Jones JDG. Molecular analysis of Agrobacterium T-DNA integration in tomato reveals a role for left border sequence homology in most integration events. Mol Genet Genomics 2007; 278:411-20. [PMID: 17574477 DOI: 10.1007/s00438-007-0259-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 05/09/2007] [Accepted: 05/25/2007] [Indexed: 11/29/2022]
Abstract
Studies in several plants have shown that Agrobacterium tumefaciens T-DNA can integrate into plant chromosomal DNA by different mechanisms involving single-stranded (ss) or double-stranded (ds) forms. One mechanism requires sequence homology between plant target and ssT-DNA border sequences and another double-strand-break repair in which preexisting chromosomal DSBs "capture" dsT-DNAs. To learn more about T-DNA integration in Solanum lycopersicum we characterised 98 T-DNA/plant DNA junction sequences and show that T-DNA left border (LB) and right border transfer is much more variable than previously reported in Arabidopsis thaliana and Populus tremula. The analysis of seven plant target sequences showed that regions of homology between the T-DNA LB and plant chromosomal DNA plays an important role in T-DNA integration. One T-DNA insertion generated a target sequence duplication that resulted from nucleolytic processing of a LB/plant DNA heteroduplex that generated a DSB in plant chromosomal DNA. One broken end contained a captured T-DNA that served as a template for DNA repair synthesis. We propose that most T-DNA integrations in tomato require sequence homology between the ssT-DNA LB and plant target DNA which results in the generation of DSBs in plant chromosomal DNA.
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Affiliation(s)
- Colwyn M Thomas
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
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Zhang J, Cai L, Cheng J, Mao H, Fan X, Meng Z, Chan KM, Zhang H, Qi J, Ji L, Hong Y. Transgene integration and organization in cotton (Gossypium hirsutum L.) genome. Transgenic Res 2007; 17:293-306. [PMID: 17549600 DOI: 10.1007/s11248-007-9101-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 04/18/2007] [Indexed: 11/28/2022]
Abstract
While genetically modified upland cotton (Gossypium hirsutum L.) varieties are ranked among the most successful genetically modified organisms (GMO), there is little knowledge on transgene integration in the cotton genome, partly because of the difficulty in obtaining large numbers of transgenic plants. In this study, we analyzed 139 independently derived T0 transgenic cotton plants transformed by Agrobacterium tumefaciens strain AGL1 carrying a binary plasmid pPZP-GFP. It was found by PCR that as many as 31% of the plants had integration of vector backbone sequences. Of the 110 plants with good genomic Southern blot results, 37% had integration of a single T-DNA, 24% had two T-DNA copies and 39% had three or more copies. Multiple copies of the T-DNA existed either as repeats in complex loci or unlinked loci. Our further analysis of two T1 populations showed that segregants with a single T-DNA and no vector sequence could be obtained from T0 plants having multiple T-DNA copies and vector sequence. Out of the 57 T-DNA/T-DNA junctions cloned from complex loci, 27 had canonical T-DNA tandem repeats, the rest (30) had deletions to T-DNAs or had inclusion of vector sequences. Overlapping micro-homology was present for most of the T-DNA/T-DNA junctions (38/57). Right border (RB) ends of the T-DNA were precise while most left border (LB) ends (64%) had truncations to internal border sequences. Sequencing of collinear vector integration outside LB in 33 plants gave evidence that collinear vector sequence was determined in agrobacterium culture. Among the 130 plants with characterized flanking sequences, 12% had the transgene integrated into coding sequences, 12% into repetitive sequences, 7% into rDNAs. Interestingly, 7% had the transgene integrated into chloroplast derived sequences. Nucleotide sequence comparison of target sites in cotton genome before and after T-DNA integration revealed overlapping microhomology between target sites and the T-DNA (8/8), deletions to cotton genome in most cases studied (7/8) and some also had filler sequences (3/8). This information on T-DNA integration in cotton will facilitate functional genomic studies and further crop improvement.
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MESH Headings
- Agrobacterium tumefaciens/genetics
- Base Sequence
- Blotting, Southern
- DNA Primers
- DNA, Bacterial/genetics
- DNA, Plant/genetics
- Genetic Vectors
- Genome, Plant
- Gossypium/genetics
- Gossypium/growth & development
- Molecular Sequence Data
- Plants, Genetically Modified
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombination, Genetic
- Repetitive Sequences, Nucleic Acid
- Reverse Transcriptase Polymerase Chain Reaction
- Transformation, Genetic
- Transgenes/physiology
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Affiliation(s)
- Jun Zhang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
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15
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Gelvin SB, Kim SI. Effect of chromatin upon Agrobacterium T-DNA integration and transgene expression. ACTA ACUST UNITED AC 2007; 1769:410-21. [PMID: 17544520 DOI: 10.1016/j.bbaexp.2007.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 04/09/2007] [Accepted: 04/12/2007] [Indexed: 11/22/2022]
Abstract
Agrobacterium tumefaciens transfers DNA (T-DNA) to plant cells, where it integrates into the plant genome. Little is known about how T-DNA chooses sites within the plant chromosome for integration. Previous studies indicated that T-DNA preferentially integrates into transcriptionally active regions of the genome, especially in 5'-promoter regions. This would make sense, considering that chromatin structure surrounding active promoters may be more "open" and accessible to foreign DNA. However, recent results suggest that this seemingly non-random pattern of integration may be an artifact of selection bias, and that T-DNA may integrate more randomly than previously thought. In this chapter, I discuss the history of these observations and the role chromatin proteins may play in T-DNA integration and transgene expression. Understanding how chromatin conformation may influence T-DNA integration will be important in developing strategies for reproducible and stable transgene expression, and for gene targeting.
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Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.
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16
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Djian-Caporalino C, Fazari A, Arguel MJ, Vernie T, VandeCasteele C, Faure I, Brunoud G, Pijarowski L, Palloix A, Lefebvre V, Abad P. Root-knot nematode (Meloidogyne spp.) Me resistance genes in pepper (Capsicum annuum L.) are clustered on the P9 chromosome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:473-86. [PMID: 17136373 DOI: 10.1007/s00122-006-0447-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 10/25/2006] [Indexed: 05/12/2023]
Abstract
The root-knot nematode (Meloidogyne spp.) is a major plant pathogen, affecting several solanaceous crops worldwide. In Capsicum annuum, resistance to this pathogen is controlled by several independent dominant genes--the Me genes. Six Me genes have previously been shown to be stable at high temperature in three highly resistant and genetically distant accessions: PI 322719, PI 201234, and CM334 (Criollo de Morelos 334). Some genes (Me4, Mech1, and Mech2) are specific to certain Meloidogyne species or populations, whereas others (Me1, Me3, and Me7) are effective against a wide range of Meloidogyne species, including M. arenaria, M. javanica, and M. incognita, the most common species in Mediterranean and tropical areas. These genes direct different response patterns in root cells depending on the pepper line and nematode species. Allelism tests and fine mapping using the BSA-AFLP approach showed these genes to be different but linked, with a recombination frequency of 0.02-0.18. Three of the PCR-based markers identified in several genetic backgrounds were common to the six Me genes. Comparative mapping with CarthaGene software indicated that these six genes clustered in a single genomic region within a 28 cM interval. Four markers were used to anchor this cluster on the P9 chromosome on an intraspecific reference map for peppers. Other disease resistance factors have earlier been mapped in the vicinity of this cluster. This genomic area is colinear to chromosome T12 of tomato and chromosome XII of potato. Four other nematode resistance genes have earlier been identified in this area, suggesting that these nematode resistance genes are located in orthologous genomic regions in Solanaceae.
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Affiliation(s)
- C Djian-Caporalino
- INRA, UMR 1064 Interactions Plantes Microorganismes et Santé Végétale, BP167, F-06903, Sophia Antipolis, France.
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17
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Hammond JP, Bowen HC, White PJ, Mills V, Pyke KA, Baker AJM, Whiting SN, May ST, Broadley MR. A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes. THE NEW PHYTOLOGIST 2006; 170:239-60. [PMID: 16608451 DOI: 10.1111/j.1469-8137.2006.01662.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Whole-genome transcriptome profiling is revealing how biological systems are regulated at the transcriptional level. This study reports the development of a robust method to profile and compare the transcriptomes of two nonmodel plant species, Thlaspi caerulescens, a zinc (Zn) hyperaccumulator, and Thlaspi arvense, a nonhyperaccumulator, using Affymetrix Arabidopsis thaliana ATH1-121501 GeneChip arrays (Affymetrix, Santa Clara, CA, USA). Transcript abundance was quantified in the shoots of agar- and compost-grown plants of both species. Analyses were optimized using a genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of Thlaspi gDNA with corresponding A. thaliana probes. In silico alignments of GeneChip probes with Thlaspi gene sequences, and quantitative real-time PCR, confirmed the validity of this approach. Approximately 5000 genes were differentially expressed in the shoots of T. caerulescens compared with T. arvense, including genes involved in Zn transport and compartmentalization. Future functional analyses of genes identified as differentially expressed in the shoots of these closely related species will improve our understanding of the molecular mechanisms of Zn hyperaccumulation.
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Affiliation(s)
- John P Hammond
- Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
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18
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Nagaya S, Kato K, Ninomiya Y, Horie R, Sekine M, Yoshida K, Shinmyo A. Expression of randomly integrated single complete copy transgenes does not vary in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2005; 46:438-44. [PMID: 15695434 DOI: 10.1093/pcp/pci039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The high variability of transgene expression is frequently observed in independent transgenic lines. Variability of transgene expression has been attributed to several factors, including differences in chromosome position, repeat sequences and copy number. The eukaryotic genome, with a heterogeneous chromatin structure, is not homogeneous for transcriptional activity. Chromatin structure at the site of integration can affect transgene expression; this phenomenon is called the position effect. In this study, we investigated whether position effects confer variability of transgene expression in Arabidopsis thaliana. We analyzed the expression of randomly integrated single 'complete' (intact, non-truncated, non-rearranged) copy transgenes in A. thaliana. Ten independent lines containing single complete copies of the transgene located at different chromosome positions showed very similar levels of transgene expression, and variability of transgene expression was not observed. This result indicates that position effects may not generally be a major cause of variability of transgene expression in A. thaliana.
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Affiliation(s)
- Shingo Nagaya
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0101 Japan
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19
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Francis KE, Spiker S. Identification of Arabidopsis thaliana transformants without selection reveals a high occurrence of silenced T-DNA integrations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 41:464-77. [PMID: 15659104 DOI: 10.1111/j.1365-313x.2004.02312.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Several recent investigations of T-DNA integration sites in Arabidopsis thaliana have reported 'cold spots' of integration, especially near centromeric regions. These observations have contributed to the ongoing debate over whether T-DNA integration is random or occurs preferentially in transcriptionally active regions. When transgenic plants are identified by selecting or screening for transgenic activity, transformants with integrations into genomic regions that suppress transcription, such as heterochromatin, may not be identified. This phenomenon, which we call selection bias, may explain the perceived non-random distribution of T-DNA integration in previous studies. In order to investigate this possibility, we have characterized the sites of T-DNA integration in the genomes of transgenic plants identified by pooled polymerase chain reaction (PCR), a procedure that does not require expression of the transgene, and is therefore free of selection bias. Over 100 transgenic Arabidopsis plants were identified by PCR and compared with kanamycin-selected transformants from the same T(1) seed pool. A higher perceived transformation efficiency and a higher frequency of transgene silencing were observed in the PCR-identified lines. Together, the data suggest approximately 30% of transformation events may result in non-expressing transgenes that would preclude identification by selection. Genomic integration sites in PCR-identified lines were compared with those in existing T-DNA integration databases. In PCR-identified lines with silenced transgenes, the integration sites mapped to regions significantly underrepresented by T-DNA integrations in studies where transformants were identified by selection. The data presented here suggest that selection bias can account for at least some of the observed non-random integration of T-DNA into the Arabidopsis genome.
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Affiliation(s)
- Kirk E Francis
- Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
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20
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Pan X, Li Y, Stein L. Site preferences of insertional mutagenesis agents in Arabidopsis. PLANT PHYSIOLOGY 2005; 137:168-75. [PMID: 15618417 PMCID: PMC548848 DOI: 10.1104/pp.104.053215] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Revised: 11/13/2004] [Accepted: 11/15/2004] [Indexed: 05/18/2023]
Abstract
We have performed a comparative analysis of the insertion sites of engineered Arabidopsis (Arabidopsis thaliana) insertional mutagenesis vectors that are based on the maize (Zea mays) transposable elements and Agrobacterium T-DNA. The transposon-based agents show marked preference for high GC content, whereas the T-DNA-based agents show preference for low GC content regions. The transposon-based agents show a bias toward insertions near the translation start codons of genes, while the T-DNAs show a predilection for the putative transcriptional regulatory regions of genes. The transposon-based agents also have higher insertion site densities in exons than do the T-DNA insertions. These observations show that the transposon-based and T-DNA-based mutagenesis techniques could complement one another well, and neither alone is sufficient to achieve the goal of saturation mutagenesis in Arabidopsis. These results also suggest that transposon-based mutagenesis techniques may prove the most effective for obtaining gene disruptions and for generating gene traps, while T-DNA-based agents may be more effective for activation tagging and enhancer trapping. From the patterns of insertion site distributions, we have identified a set of nucleotide sequence motifs that are overrepresented at the transposon insertion sites. These motifs may play a role in the transposon insertion site preferences. These results could help biologists to study the mechanisms of insertions of the insertional mutagenesis agents and to design better strategies for genome-wide insertional mutagenesis.
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Affiliation(s)
- Xiaokang Pan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
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21
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Labra M, Vannini C, Grassi F, Bracale M, Balsemin M, Basso B, Sala F. Genomic stability in Arabidopsis thaliana transgenic plants obtained by floral dip. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:1512-1518. [PMID: 15300384 DOI: 10.1007/s00122-004-1773-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2004] [Accepted: 07/08/2004] [Indexed: 05/24/2023]
Abstract
The occurrence of DNA modification is an undesired phenomenon accompanying plant cell transformation. The event has been correlated with the stress imposed by the presently utilised transformation procedures, all depending on plant differentiation from in vitro cell culture, but other causes have not been excluded. In this work, transgenic Arabidopsis thaliana plants have been produced by an approach that does not require cell dedifferentiation, being based on in planta Agrobacterium-mediated gene transfer by flower infiltration, which is followed by recovery and selection of transgenic progeny. Genomic DNA changes in transgenic and control plants have been investigated by AFLP and RAMP analysis. Results show no statistically relevant genomic modifications in transgenic plants, as compared with control untreated plants. Variations were observed in callus-derived A. thaliana plants, thus supporting the conclusion that somaclonal variation is essentially correlated with the stress imposed by the in vitro cell culture, rather than with the integration of a foreign gene.
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Affiliation(s)
- M Labra
- Department of Environmental Science, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
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22
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Cellini F, Chesson A, Colquhoun I, Constable A, Davies HV, Engel KH, Gatehouse AMR, Kärenlampi S, Kok EJ, Leguay JJ, Lehesranta S, Noteborn HPJM, Pedersen J, Smith M. Unintended effects and their detection in genetically modified crops. Food Chem Toxicol 2004; 42:1089-125. [PMID: 15123383 DOI: 10.1016/j.fct.2004.02.003] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2003] [Accepted: 02/04/2004] [Indexed: 11/28/2022]
Abstract
The commercialisation of GM crops in Europe is practically non-existent at the present time. The European Commission has instigated changes to the regulatory process to address the concerns of consumers and member states and to pave the way for removing the current moratorium. With regard to the safety of GM crops and products, the current risk assessment process pays particular attention to potential adverse effects on human and animal health and the environment. This document deals with the concept of unintended effects in GM crops and products, i.e. effects that go beyond that of the original modification and that might impact primarily on health. The document first deals with the potential for unintended effects caused by the processes of transgene insertion (DNA rearrangements) and makes comparisons with genetic recombination events and DNA rearrangements in traditional breeding. The document then focuses on the potential value of evolving "profiling" or "omics" technologies as non-targeted, unbiased approaches, to detect unintended effects. These technologies include metabolomics (parallel analysis of a range of primary and secondary metabolites), proteomics (analysis of polypeptide complement) and transcriptomics (parallel analysis of gene expression). The technologies are described, together with their current limitations. Importantly, the significance of unintended effects on consumer health are discussed and conclusions and recommendations presented on the various approaches outlined.
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Affiliation(s)
- F Cellini
- Metapontum Agrobios, SS Jonica Km 448.2, I-75010 Metaponto Matera, Italy
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23
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Chen S, Jin W, Wang M, Zhang F, Zhou J, Jia Q, Wu Y, Liu F, Wu P. Distribution and characterization of over 1000 T-DNA tags in rice genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 36:105-13. [PMID: 12974815 DOI: 10.1046/j.1365-313x.2003.01860.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We generated T-DNA insertions throughout the rice genome for saturation mutagenesis. More than 1,000 flanking sequences were mapped on 12 rice chromosomes. Our results showed that T-DNA tags were not randomly spread on rice chromosomes and were preferentially inserted in gene-rich regions. Few insertions (2.4%) were found in repetitive regions. T-DNA insertions in genic (58.1%) and intergenic regions (41.9%) showed a good correlation with the predicted size distribution of these sequences in the rice genome. Whereas, obvious biases were found for the insertions in the 5'- and 3'-regulatory regions outside the coding regions both at 500-bp size and in introns rather than in exons. Such distribution patterns and biases for T-DNA integration in rice are similar to that of the previous report in Arabidopsis, which may result from T-DNA integration mechanism itself. Rice will require approximately the same number of T-DNA insertions for saturation mutagenesis as will Arabidopsis. A database of the T-DNA insertion sites in rice is publicly available at our web site (http://www.genomics.zju.edu.cn/ricetdna).
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Affiliation(s)
- Shuangyan Chen
- The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310029, China
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24
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Urban M, Mott E, Farley T, Hammond-Kosack K. The Fusarium graminearum MAP1 gene is essential for pathogenicity and development of perithecia. MOLECULAR PLANT PATHOLOGY 2003; 4:347-59. [PMID: 20569395 DOI: 10.1046/j.1364-3703.2003.00183.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
SUMMARY Fusarium graminearum is the causal agent of ear blight disease of cereals. Infection occurs at anthesis when ascospores and/or conidia directly penetrate exposed anther and ovary tissue. The hemibiotrophic hyphae colonize floral tissues and developing grains to cause premature ear senescence. During infection, Fusarium hyphae can also produce hazardous trichothecene mycotoxins, thereby posing a threat to human and animal health and safety. The Fusarium MAP1 gene was identified using a PCR approach by its homology to a known pathogenicity gene of Magnaporthe grisea, the mitogen-activated protein kinase gene PMK1. Gene replacement F. graminearum map1 mutants were non-pathogenic on wheat flowers and roots, and also could not infect wounded wheat floral tissue or tomato fruits. Unlike the wild-type strain, map1 mutant inoculations did not compromise grain yield. Map1 mutants lost their ability to form perithecia in vitro, but their rate of asexual conidiation was unaffected. DON mycotoxin production in planta was still detected. Collectively, the observed phenotypes suggest that the Map1 signalling protein controls multiple events in disease establishment and propagation. Novel approaches to control Fusarium ear blight disease by blocking perithecial development are discussed.
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Affiliation(s)
- Martin Urban
- Plant-Pathogen Interactions Division, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
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25
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Jung KH, Hur J, Ryu CH, Choi Y, Chung YY, Miyao A, Hirochika H, An G. Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system. PLANT & CELL PHYSIOLOGY 2003; 44:463-72. [PMID: 12773632 DOI: 10.1093/pcp/pcg064] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have previously generated a large pool of T-DNA insertional lines in rice. In this study, we screened those T-DNA pools for rice mutants that had defective chlorophylls. Among the 1,995 lines examined in the T2 generation, 189 showed a chlorophyll-deficient phenotype that segregated as a single recessive locus. Among the mutants, 10 lines were beta-glucuronidase (GUS)-positive in the leaves. Line 9-07117 has a T-DNA insertion into the gene that is highly homologous to XANTHA-F in barley and CHLH in Arabidopsis: This OsCHLH gene encodes the largest subunit of the rice Mg-chelatase, a key enzyme in the chlorophyll branch of the tetrapyrrole biosynthetic pathway. In the T2 and T3 generations, the chlorina mutant phenotypes are co-segregated with the T-DNA. We have identified two additional chlorina mutants that have a Tos17 insertion in the OsCHLH gene. Those phenotypes were co-segregated with Tos17 in the progeny. GUS assays and RNA blot analysis showed that expression of the OsCHLH gene is light inducible, while TEM analysis revealed that the thylakoid membrane of the mutant chloroplasts is underdeveloped. The chlorophyll content was very low in the OschlH mutants. This is the first report that T-DNA insertional mutagenesis can be used for functional analysis of rice genes.
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Affiliation(s)
- Ki-Hong Jung
- National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 790-784 Republic of Korea
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26
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Garcia V, Bruchet H, Camescasse D, Granier F, Bouchez D, Tissier A. AtATM is essential for meiosis and the somatic response to DNA damage in plants. THE PLANT CELL 2003; 15:119-32. [PMID: 12509526 PMCID: PMC143473 DOI: 10.1105/tpc.006577] [Citation(s) in RCA: 211] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2002] [Accepted: 10/25/2002] [Indexed: 05/17/2023]
Abstract
In contrast to yeast or mammalian cells, little is known about the signaling responses to DNA damage in plants. We previously characterized AtATM, an Arabidopsis homolog of the human ATM gene, which is mutated in ataxia telangiectasia, a chromosome instability disorder. The Atm protein is a protein kinase whose activity is induced by DNA damage, particularly DNA double-strand breaks. The phosphorylation targets of Atm include proteins involved in DNA repair, cell cycle control, and apoptosis. Here, we describe the isolation and functional characterization of two Arabidopsis mutants carrying a T-DNA insertion in AtATM. Arabidopsis atm mutants are hypersensitive to gamma-radiation and methylmethane sulfonate but not to UV-B light. In correlation with the radiation sensitivity, atm mutants failed to induce the transcription of genes involved in the repair and/or detection of DNA breaks upon irradiation. In addition, atm mutants are partially sterile, and we show that this effect is attributable to abundant chromosomal fragmentation during meiosis. Interestingly, the transcription of DNA recombination genes during meiosis was not dependent on AtATM, and meiotic recombination occurred at the same rate as in wild-type plants, raising questions about the function of AtAtm during meiosis in plants. Our results demonstrate that AtATM plays a central role in the response to both stress-induced and developmentally programmed DNA damage.
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Affiliation(s)
- Valérie Garcia
- Laboratoire de Radiobiologie Végétale, Département d'Ecophysiologie Végétale et de Microbiologie, Commissariat à l'Energie Atomique, 13108 St. Paul-lez-Durance Cedex, France
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27
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Bundock P, van Attikum H, den Dulk-Ras A, Hooykaas PJJ. Insertional mutagenesis in yeasts using T-DNA from Agrobacterium tumefaciens. Yeast 2002; 19:529-36. [PMID: 11921101 DOI: 10.1002/yea.858] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Insertional mutagenesis is a powerful tool for the isolation of novel mutations. The gene delivery system of the bacterium Agrobacterium tumefaciens, which mediates transfer not only to plants but also to yeasts and fungi, could be exploited to generate collections of yeasts containing insertional mutations if there were no bias towards particular integration sites, as is the case in plants. To test this, we have analysed a small collection of Saccharomyces cerevisiae strains with T-DNA copies integrated in the S. cerevisiae genome. The position of 54 of these T-DNAs was determined. The T-DNA showed no clear preference for certain DNA sequences or genomic regions. We have isolated insertions in the coding regions of the genes YGR125w, YDR250c, YGR141w, YGR045c, YPL017c, YGR040w, YDL052c, YJL148w, YCL033c, YFL061w, YJR033c, YDR175c and YLR309c confirming that these genes are non-essential for S. cerevisiae haploid growth on minimal medium. Given the advantages of T-DNA, we propose its use as an ideal mobile DNA element for insertional mutagenesis in yeasts.
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Affiliation(s)
- Paul Bundock
- Institute for Molecular Plant Sciences, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands.
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28
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Emmanuel E, Levy AA. Tomato mutants as tools for functional genomics. CURRENT OPINION IN PLANT BIOLOGY 2002; 5:112-117. [PMID: 11856605 DOI: 10.1016/s1369-5266(02)00237-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Tomato mutants have been used in genetic studies and breeding for decades, yet only a few tomato mutants have been characterized at the molecular level. Similarly, a wealth of sequence information for tomato is now available but the functions of only a few genes are known. New developments - such as the use of saturated mutant populations, new methods for the detection of mutants and new sequence data - are bridging the gap between tomato genes and their functions.
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Affiliation(s)
- Eyal Emmanuel
- Department of Plant Sciences, Weizmann Institute of Sciences, Rehovot, Israel
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29
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Tax FE, Vernon DM. T-DNA-associated duplication/translocations in Arabidopsis. Implications for mutant analysis and functional genomics. PLANT PHYSIOLOGY 2001; 126:1527-38. [PMID: 11500551 PMCID: PMC117152 DOI: 10.1104/pp.126.4.1527] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2001] [Revised: 03/23/2001] [Accepted: 04/26/2001] [Indexed: 05/18/2023]
Abstract
T-DNA insertion mutants have become a valuable resource for studies of gene function in Arabidopsis. In the course of both forward and reverse genetic projects, we have identified novel interchromosomal rearrangements in two Arabidopsis T-DNA insertion lines. Both rearrangements were unilateral translocations associated with the left borders of T-DNA inserts that exhibited normal Mendelian segregation. In one study, we characterized the embryo-defective88 mutation. Although emb88 had been mapped to chromosome I, molecular analysis of DNA adjacent to the T-DNA left border revealed sequence from chromosome V. Simple sequence length polymorphism mapping of the T-DNA insertion demonstrated that a >40-kbp region of chromosome V had inserted with the T-DNA into the emb88 locus on chromosome I. A similar scenario was observed with a prospective T-DNA knockout allele of the LIGHT-REGULATED RECEPTOR PROTEIN KINASE (LRRPK) gene. Whereas wild-type LRRPK is on lower chromosome IV, mapping of the T-DNA localized the disrupted LRRPK allele to chromosome V. In both these cases, the sequence of a single T-DNA-flanking region did not provide an accurate picture of DNA disruption because flanking sequences had duplicated and inserted, with the T-DNA, into other chromosomal locations. Our results indicate that T-DNA insertion lines--even those that exhibit straightforward genetic behavior--may contain an unexpectedly high frequency of rearrangements. Such duplication/translocations can interfere with reverse genetic analyses and provide misleading information about the molecular basis of mutant phenotypes. Simple mapping and polymerase chain reaction methods for detecting such rearrangements should be included as a standard step in T-DNA mutant analysis.
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Affiliation(s)
- F E Tax
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
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30
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Mercier R, Vezon D, Bullier E, Motamayor JC, Sellier A, Lefèvre F, Pelletier G, Horlow C. SWITCH1 (SWI1): a novel protein required for the establishment of sister chromatid cohesion and for bivalent formation at meiosis. Genes Dev 2001; 15:1859-71. [PMID: 11459834 PMCID: PMC312743 DOI: 10.1101/gad.203201] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2001] [Accepted: 05/18/2001] [Indexed: 11/25/2022]
Abstract
We have characterized a new gene, SWI1, involved in sister chromatid cohesion during both male and female meiosis in Arabidopsis thaliana. A first allele, swi1.1, was obtained as a T-DNA tagged mutant and was described previously as abnormal exclusively in female meiosis. We have isolated a new allele, swi1.2, which is defective for both male and female meiosis. In swi1.2 male meiosis, the classical steps of prophase were not observed, especially because homologs do not synapse. Chromatid arms and centromeres lost their cohesion in a stepwise manner before metaphase I, and 20 chromatids instead of five bivalents were seen at the metaphase plate, which was followed by an aberrant segregation. In contrast, swi1.2 female meiocytes performed a mitotic-like division instead of meiosis, indicating a distinct role for SWI1 or a different effect of the loss of SWI1 function in both processes. The SWI1 gene was cloned; the putative SWI1 protein did not show strong similarity to any known protein. Plants transformed with a SWI1-GFP fusion indicated that SWI1 protein is present in meiocyte nuclei, before meiosis and at a very early stage of prophase. Thus, SWI1 appears to be a novel protein involved in chromatid cohesion establishment and in chromosome structure during meiosis, but with clear differences between male and female meiosis.
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Affiliation(s)
- R Mercier
- Station de Génétique et d'Amélioration des Plantes, Institut National de la Recherche Agronomique, Route de Saint-Cyr, 78026 Versailles cedex, France.
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Barakat A, Gallois P, Raynal M, Mestre-Ortega D, Sallaud C, Guiderdoni E, Delseny M, Bernardi G. The distribution of T-DNA in the genomes of transgenic Arabidopsis and rice. FEBS Lett 2000; 471:161-4. [PMID: 10767414 DOI: 10.1016/s0014-5793(00)01393-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Almost all the nuclear genes of four Gramineae (maize, wheat, barley, rice) and pea are located in DNA fractions covering only a 1-2% GC range and representing between 10 and 25% of the different genomes. These DNA fractions comprise large gene-rich regions (collectively called the 'gene space') separated by vast gene-empty, repeated sequences. In contrast, in Arabidopsis thaliana, genes are distributed in DNA fractions covering an 8% GC range and representing 85% of the genome. Here, we investigated the integration of a transferred DNA (T-DNA) in the genomes of Arabidopsis and rice and found different patterns of integration, which are correlated with the different gene distributions. While T-DNA integrates essentially everywhere in the Arabidopsis genome, integration was detected only in the gene space, namely in the gene-rich, transcriptionally active, regions of the rice genome. The implications of these results for the integration of foreign DNA are discussed.
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Affiliation(s)
- A Barakat
- Laboratoire de Biologie Moléculaire et Physiologie Végétale, Université de Perpignan, 52 Avenue Villeneuve, 66000, Perpignan, France
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32
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Aranda MA, Escaler M, Thomas CL, Maule AJ. A heat shock transcription factor in pea is differentially controlled by heat and virus replication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 20:153-61. [PMID: 10571875 DOI: 10.1046/j.1365-313x.1999.00586.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Since some heat-inducible genes [heat shock (hs) genes] can be induced by virus infection in pea [e.g. Hsp70; Aranda et al. 1996, Proc. Natl Acad. Sci. USA 93, 15289-15293], we have investigated the effect that heat and virus replication may have on the expression of a heat-shock transcription factor gene (Hsf). We have characterized what appears to be the only member of the Hsf family in pea, PsHsfA. Similar to Hsp70, PsHsfA is heat-inducible in vegetative and embryonic tissues, which is concordant with the presence of heat shock elements (HSEs) and stress responsive elements (STREs) on its promoter sequence. The expression of PsHsfA during virus replication was studied in pea cotyledons and leaves, and compared to that of Hsp70. In situ hybridization experiments showed that whereas Hsp70 is induced, there is no detectable increased accumulation of PsHsfA RNA associated with the replication of pea seed-borne mosaic potyvirus (PSbMV). These experiments indicate that there is a selective control of virus-induced hs gene expression, and suggest that different regulatory pathways control hs gene expression during heat shock and virus replication.
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Affiliation(s)
- M A Aranda
- John Innes Centre, Norwich Research Park, Colney, UK
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33
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Conner AJ, Jacobs JM. Genetic engineering of crops as potential source of genetic hazard in the human diet. Mutat Res 1999; 443:223-34. [PMID: 10415441 DOI: 10.1016/s1383-5742(99)00020-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The benefits of genetic engineering of crop plants to improve the reliability and quality of the world food supply have been contrasted with public concerns raised about the food safety of the resulting products. Debates have concentrated on the possible unforeseen risks associated with the accumulation of new metabolites in crop plants that may contribute to toxins, allergens and genetic hazards in the human diet. This review examines the various molecular and biochemical mechanisms by which new hazards may appear in foods as a direct consequence of genetic engineering in crop plants. Such hazards may arise from the expression products of the inserted genes, secondary or pleiotropic effects of transgene expression, and random insertional mutagenic effects resulting from transgene integration into plant genomes. However, when traditional plant breeding is evaluated in the same context, these mechanisms are no different from those that have been widely accepted from the past use of new cultivars in agriculture. The risks associated with the introduction of new genes via genetic engineering must be considered alongside the common breeding practice of introgressing large fragments of chromatin from related wild species into crop cultivars. The large proportion of such introgressed DNA involves genes of unknown function linked to the trait of interest such as pest or disease resistance. In this context, the potential risks of introducing new food hazards from the applications of genetic engineering are no different from the risks that might be anticipated from genetic manipulation of crops via traditional breeding. In many respects, the precise manner in which genetic engineering can control the nature and expression of the transferred DNA offers greater confidence for producing the desired outcome compared with traditional breeding.
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Affiliation(s)
- A J Conner
- New Zealand Institute for Crop and Food Research, Private Bag 4704, Christchurch, New Zealand
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34
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Laufs P, Autran D, Traas J. A chromosomal paracentric inversion associated with T-DNA integration in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 18:131-9. [PMID: 10363366 DOI: 10.1046/j.1365-313x.1999.00436.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
T-DNA integration in the nuclear plant genome may lead to rearrangements of the plant target site. Here we present evidence for a chromosomal inversion of 26 cM bordered by two T-DNAs in direct orientation, which is linked to the mgoun2 mutation. The integration sites of the T-DNAs map at positions 80 and 106 of chromosome I and we show that each T-DNA is bordered by plant sequences from positions 80 and 106, respectively. Although the T-DNAs are physically distant, they are genetically closely linked. In addition, three markers located on the chromosome segment between the two T-DNA integration sites show no recombination with the mgo2 mutation. We show that the inversion cannot be a consequence of a recombination event between the two T-DNAs, but that the integration of the T-DNAs and the inversion were two temporally linked events. T-DNA integration mechanisms that could have led to this inversion are discussed.
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Affiliation(s)
- P Laufs
- Institut National de la Recherche Agronomique, Laboratoire de Biologie Cellulaire, Versailles, France.
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35
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Parniske M, Wulff BB, Bonnema G, Thomas CM, Jones DA, Jones JD. Homologues of the Cf-9 disease resistance gene (Hcr9s) are present at multiple loci on the short arm of tomato chromosome 1. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1999; 12:93-102. [PMID: 9926411 DOI: 10.1094/mpmi.1999.12.2.93] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The tomato Cf-4 and Cf-9 genes map at a genetically complex locus on the short arm of chromosome 1 and confer resistance against Cladosporium fulvum through recognition of different pathogen-encoded avirulence determinants. Cf-4 and Cf-9 are members of a large gene family (Hcr9s, Homologues of Cladosporium fulvum resistance gene Cf-9), some of which encode additional distinct recognition specificities. A genetic analysis of the majority of Hcr9s suggests that their distribution is spatially restricted to the short arm of chromosome 1. Two loci of clustered Hcr9 genes have been analyzed physically that mapped distal (Northern Lights) and proximal (Southern Cross) to the Cf-4/9 locus (Milky Way). Sequence homologies between intergenic regions at Southern Cross and Milky Way indicate local Hcr9 duplication preceded cluster multiplication. The multiplication of clusters involved DNA flanking Hcr9 sequences as indicated by conserved lipoxygenase sequences at Southern Cross and Milky Way. The similar spatial distribution of Hcr9 clusters in different Lycopersicon spp. suggests Hcr9 cluster multiplication preceded speciation.
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Affiliation(s)
- M Parniske
- Sainsbury Laboratory, John Innes Centre, Norwich, U.K
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36
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Takken FL, Schipper D, Nijkamp HJ, Hille J. Identification and Ds-tagged isolation of a new gene at the Cf-4 locus of tomato involved in disease resistance to Cladosporium fulvum race 5. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 14:401-411. [PMID: 9670557 DOI: 10.1046/j.1365-313x.1998.00135.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Leaf mould disease in tomato is caused by the biotrophic fungus Cladosporium fulvum. An Ac/Ds targeted transposon tagging strategy was used to isolate the gene conferring resistance to race 5 of C. fulvum, a strain expressing the avirulence gene Avr4. An infection assay of 2-week-old seedlings yielded five susceptible mutants, of which two had a Ds element integrated in the same gene at different positions. This gene, member of a gene family, showed high sequence homology to the C. fulvum resistance genes Cf-9 and Cf-2. The gene is predicted to encode an extracellular transmembrane protein containing a divided domain of 25 leucine-rich repeats. Three mutants exhibited a genomic deletion covering most of the Lycopersicon hirsutum introgressed segment, including the Cf-4 locus. Southern blot analysis revealed that this deletion includes the tagged gene and five homologous sequences. To test whether the tagged gene confers resistance to C. fulvum via Avr4 recognition, the Avr4 gene was expressed in planta. Surprisingly, expression of the Avr4 gene still triggered a specific necrotic response in the transposon-tagged plants, indicating that the tagged resistance gene is not, or is not the only gene, involved in Avr4 recognition. Mutants harbouring the genomic deletion did not show this Avr4-specific response. The deleted segment apparently contains, in addition to the tagged gene, one or more other genes, which play a role in the Avr4 responses. The tagged gene is present at the Cf-4 locus, but it does not necessarily recognize Avr4 and is therefore designated Cf-4A.
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Affiliation(s)
- F L Takken
- Department of Genetics, BioCentrum Amsterdam, Vrije Universiteit, The Netherlands.
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37
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English JJ, Jones JD. Epigenetic instability and trans-silencing interactions associated with an SPT::Ac T-DNA locus in tobacco. Genetics 1998; 148:457-69. [PMID: 9475755 PMCID: PMC1459778 DOI: 10.1093/genetics/148.1.457] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Progeny of tobacco line 2853.6, which carries a streptomycin phosphotransferase (SPT) gene interrupted by the maize element Activator (Ac), were selected for streptomycin resistance (Spr) because of germinal Ac excision. Some events gave rise to Spr alleles that were unstable and exhibited a mottled phenotype on streptomycin-containing medium due to somatic loss of SPT function. This instability was most pronounced in one particular line, Spr12F. Other Spr alleles rarely exhibited silencing of SPT. Streptomycin-sensitive, homozygous Spr12F plants were recovered, and crosses were performed with other, more stable Spr lines. A high proportion of the resulting heterozygous progeny were silenced for SPT expression. The silenced state was heritable even after the Spr12F allele segregated away. No correlation could be made between silencing and methylation of the SPTgene. Structural analysis of allele Spr12F showed that the SPT gene from which Ac had excised was flanked by direct repeats of Ac. A search was carried out among 110 additional Spr alleles for new independent unstable alleles, and four were identified. All of these alleles also carried an SPT gene flanked by direct repeats of Ac. Thus, there is a strong correlation between this structure and instability of SPT expression.
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Affiliation(s)
- J J English
- The Sainsbury Laboratory, John Innes Centre, Norwich, United Kingdom
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38
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Spassieva S, Brandwagt B, Stoyanova R, Dukjandjiev S, Hille J. The Ac/DsTransposon System from Maize as a Tool for Generating Mutant Phenotypes in Tomato ( Lycopersicon Esculentum). BIOTECHNOL BIOTEC EQ 1998. [DOI: 10.1080/13102818.1998.10818959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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39
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Okubara PA, Arroyo-Garcia R, Shen KA, Mazier M, Meyers BC, Ochoa OE, Kim S, Yang CH, Michelmore RW. A transgenic mutant of Lactuca sativa (lettuce) with a T-DNA tightly linked to loss of downy mildew resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1997; 10:970-7. [PMID: 9353944 DOI: 10.1094/mpmi.1997.10.8.970] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
One hundred and ninety-two independent primary transformants of lettuce cv. Diana were obtained by co-cultivation with Agrobacterium tumefaciens carrying constructs containing maize Ac transposase and Ds. R2 families were screened for mutations at four genes (Dm) for resistance to downy mildew. One family, designated dm3t524, had lost resistance to an isolate of Bremia lactucae expressing the avirulence gene Avr3. Loss of resistance segregated as a single recessive allele of Dm3. The mutation was not due to a large deletion as all molecular markers flanking Dm3 were present. Loss of Dm3 activity co-segregated with a T-DNA from which Ds had excised. Genomic DNA flanking the right border of this T-DNA was isolated by inverse polymerase chain reaction. This genomic sequence was present in four to five copies in wild-type cv. Diana. One copy was missing in all eight deletion mutants of Dm3 and altered in dm3t524, indicating tight physical linkage to Dm3. Three open reading frames (ORFs) occurred in a 6.6-kb region flanking the insertion site; however, expression of these ORFs was not detected. No similarities were detected between these ORFs and resistance genes cloned from other species. Transgenic complementation with 11-to 27-kb genomic fragments of Diana spanning the insertion site failed to restore Dm3 function to two ethyl methanesulfonate (EMS)-induced mutants of Dm3 or to cv. Cobham Green, which naturally lacks Dm3 activity. Therefore, either the T-DNA inserted extremely close to, but not within, Dm3 and the mutation may have been caused by secondary movement of Ds, or Dm3 activity is encoded by a gene extending beyond the fragments used for complementation.
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Affiliation(s)
- P A Okubara
- Department of Vegetable Crops, University of California, Davis 95616, USA
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40
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Van Lijsebettens M, Wang X, Cnops G, Boerjan W, Desnos T, Höfte H, Van Montagu M. Transgenic Arabidopsis tester lines with dominant marker genes. MOLECULAR & GENERAL GENETICS : MGG 1996; 251:365-72. [PMID: 8676880 DOI: 10.1007/bf02172528] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The map positions of a set of eight T-DNA insertions in the Arabidopsis genome have been determined by using closely linked visible markers. The insertions are dispersed over four of the five chromosomes. Each T-DNA insert contains one or more of the chimeric marker genes neomycin phosphotransferase (neo), hygromycin phosphotransferase (hpt), phosphinothricin acetyltransferase (bar), beta-glucuronidase (gusA) and indole-3-acetamide hydrolase (iaaH). The neo, hpt and bar marker genes are dominant in a selective germination assay or when used as DNA markers in a polymerase chain reaction. These dominant markers will allow recombinants to be discerned in a germinating F2 population, one generation earlier than with a conventional recessive marker. The transgenic marker lines will speed up and simplify the isolation of recombinants in small genetic intervals, a rate-limiting step in positional cloning strategies. The transgenic lines containing the hpt marker will also be of interest for the isolation of deletion mutants at the T-DNA integration sites.
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41
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van der Biezen EA, Brandwagt BF, van Leeuwen W, Nijkamp HJ, Hille J. Identification and isolation of the FEEBLY gene from tomato by transposon tagging. MOLECULAR & GENERAL GENETICS : MGG 1996; 251:267-80. [PMID: 8676869 DOI: 10.1007/bf02172517] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Ac/Ds transposon system from maize was used for insertional mutagenesis in tomato. Marker genes were employed for the selection of plants carrying a total of 471 unique Ds elements. Three mutants were obtained with Ds insertions closely linked to recessive mutations: feebly (fb), yellow jim (yj) and dopey (dp). The fb seedlings produced high anthocyanin levels, developed into small fragile plants, and were insensitive to the herbicide phosphinothricin. The yj plants had yellow leaves as a result of reduced levels of chlorophyll. The dp mutants completely or partially lacked inflorescences. The fb and yj loci were genetically linked to the Ds donor site on chromosome 3. Reactivation of the Ds element in the fb mutants by crosses with an Ac-containing line resulted in restoration of the wild-type phenotypes. Plant DNA fragments flanking both sides of the Ds element in the fb mutant were isolated by the inverse polymerase chain reaction. Molecular analysis showed that phenotypic reversions of fb were correlated with excisions of Ds. DNA sequence analysis of Fb reversion alleles showed the characteristic Ds footprints. Northern and cDNA sequence analysis indicated that transcription of the FEEBLY (FB) gene was impeded by the insertion of Ds in an intron. Comparison of the predicted amino acid sequence of the FB protein with other database sequences indicated that FB is a novel gene.
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42
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Burbidge A, Grieve TM, Woodman KJ, Taylor IB. Strategies for targeted transposon tagging of ABA biosynthetic mutants in tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:1022-1031. [PMID: 24169992 DOI: 10.1007/bf00223915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/1995] [Accepted: 03/17/1995] [Indexed: 06/02/2023]
Abstract
The ABA biosynthetic pathway has been studied in detail and the steps impaired in some ABA-deficient mutants are known. However, little is known of the molecular control mechanisms regulating ABA production in planta. A direct route for improving our understanding of these mechanisms is to transposon tag and clone the wild-type counterparts of the ABA mutant alleles. On the basis of the observation that maize transposons move preferentially to linked sites in both homologous and heterologous systems and in doing so disrupt gene function, a targeted transposon mutagenesis strategy is being developed towards cloning ABA biosynthetic genes from tomato. The possibility of using marker genes to identify T-DNA insertion sites in selected parts of the genome has been examined and compared with an inverse PCR/RFLP approach to mapping T-DNAs.
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Affiliation(s)
- A Burbidge
- Department of Physiology and Environmental Science, Faculty of Agriculture and Food Sciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, Loughborough, Leicestershire, UK
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43
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Bríza J, Carroll BJ, Klimyuk VI, Thomas CM, Jones DA, Jones JD. Distribution of unlinked transpositions of a Ds element from a T-DNA locus on tomato chromosome 4. Genetics 1995; 141:383-90. [PMID: 8536985 PMCID: PMC1206735 DOI: 10.1093/genetics/141.1.383] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In maize, receptor sites for unlinked transpositions of Activator (Ac) elements are not distributed randomly. To test whether the same is true in tomato, the receptor sites for a Dissociation (Ds) element derived from Ac, were mapped for 26 transpositions unlinked to a donor T-DNA locus on chromosome 4. Four independent transposed Dss mapped to sites on chromosome 4 genetically unlinked to the donor T-DNA, consistent with a preference for transposition to unlinked sites on the same chromosome as opposed to sites on other chromosomes. There was little preference among the nondonor chromosomes, except perhaps for chromosome 2, which carried seven transposed Dss, but these could not be proven to be independent. However, these data, when combined with those from other studies in tomato examining the distribution of transposed Acs or Dss among nondonor chromosomes, suggest there may be absolute preferences for transposition irrespective of the chromosomal location of the donor site. If true, transposition to nondonor chromosomes in tomato would differ from that in maize, where the preference seems to be determined by the spatial arrangement of chromosomes in the interphase nucleus. The tomato lines carrying Ds elements at known locations are available for targeted transposon tagging experiments.
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Affiliation(s)
- J Bríza
- Sainsbury Laboratory, John Innes Centre, Norwich, United Kingdom
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44
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Robbins TP, Gerats AG, Fiske H, Jorgensen RA. Suppression of recombination in wide hybrids of Petunia hybrida as revealed by genetic mapping of marker transgenes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 90:957-968. [PMID: 24173050 DOI: 10.1007/bf00222909] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/1994] [Accepted: 12/08/1994] [Indexed: 06/02/2023]
Abstract
In the course of a heterologous transposon tagging experiment in Petunia hybrida (n=7), 135 independent T-DNA loci were tested for linkage to the target genes Hf1 and Fl, which are located on the two largest chromosomes. Approximately one-third (47) of these T-DNA loci were linked to one of these two markers. Of these 47 linkedloci, 19 mapped within 1 cM of its marker, indicating a highly non-random genetic distribution of introduced loci. However, rather than non-random integration within both of the marked chromosomes, this probably reflects a suppression of recombination around these marker loci in the particular wide hybrids used for mapping. This hypothesis was tested by measuring recombination between linked T-DNAs in an inbred background. Inbred recombination levels were found to be at least 3-fold higher around the Hf1 locus and 12-fold higher around Fl compared to the wide hybrids. These findings may reflect the origin of P. hybrida by hybridization of wild species, and while relevant to genetic mapping in petunia in particular they may also have more general significance for any mapping strategies involving the use of wide hybrids in other species.
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Affiliation(s)
- T P Robbins
- DNA Plant Technology Corporation, 6701 San Pablo Avenue, 94608, Oakland, CA, USA
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45
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Osborne BI, Baker B. Movers and shakers: maize transposons as tools for analyzing other plant genomes. Curr Opin Cell Biol 1995; 7:406-13. [PMID: 7662372 DOI: 10.1016/0955-0674(95)80097-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Transposons have been successfully exploited as insertional mutagens for the efficient identification and isolation of genes (transposon tagging) in many organisms. Plants are no exception. The maize Activator and Suppressor-mutator transposons function when transferred into heterologous plant species, and many different gene tagging systems have been developed. These systems have recently been used to clone novel and important genes, including disease resistance loci from Nicotiana tabacum, tomato and flax.
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Affiliation(s)
- B I Osborne
- Plant Gene Expression Center, Albany, California, USA
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46
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van der Biezen EA, Glagotskaya T, Overduin B, Nijkamp HJ, Hille J. Inheritance and genetic mapping of resistance to Alternaria alternata f. sp. lycopersici in Lycopersicon pennellii. MOLECULAR & GENERAL GENETICS : MGG 1995; 247:453-61. [PMID: 7770053 DOI: 10.1007/bf00293147] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The fungal pathogen Alternaria alternata f. sp. lycopersici produces AAL-toxins that function as chemical determinants of the Alternaria stem canker disease in the tomato (Lycopersicon esculentum). In resistant cultivars, the disease is controlled by the Asc locus on chromosome 3. Our aim was to characterize novel sources of resistance to the fungus and of insensitivity to the host-selective AAL-toxins. To that end, the degree of sensitivity of wild tomato species to AAL-toxins was analyzed. Of all members of the genus Lycopersicon, only L. cheesmanii was revealed to be sensitive to AAL-toxins and susceptible to fungal infection. Besides moderately insensitive responses from some species, L. pennellii and L. peruvianum were shown to be highly insensitive to AAL-toxins as well as resistant to the pathogen. Genetic analyses showed that high insensitivity to AAL-toxins from L. pennellii is inherited in tomato as a single complete dominant locus. This is in contrast to the incomplete dominance of insensitivity to AAL-toxins of L. esculentum. Subsequent classical genetics, RFLP mapping and allelic testing indicated that high insensitivity to AAL-toxins from L. pennellii is conferred by a new allele of the Asc locus.
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47
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Balint-Kurti PJ, Dixon MS, Jones DA, Norcott KA, Jones JD. RFLP linkage analysis of the Cf-4 and Cf-9 genes for resistance toCladosporium fulvum in tomato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 88:691-700. [PMID: 24186164 DOI: 10.1007/bf01253972] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/1993] [Accepted: 11/10/1993] [Indexed: 06/02/2023]
Abstract
Four different populations segregating for one of the two closely linked (possibly allelic) tomato disease resistance genes to the fungusCladosporium fulvum,Cf-4 andCf-9, were generated and analysed for recombination frequencies between theCf-genes and restriction fragment length polymorphism (RFLP) loci. The population consisting of F2 progeny from the interspecific crossLycopersicon esculentum carryingCf-9 ×L. pennellii was identified as the most useful for RFLP mapping of theCf-4/9 locus and an RFLP map around this locus was constructed mainly using this population. The two closest markers identified were CP46, 2.6 cM distal, and a group of 11 markers including TG236, 3.7 cM proximal toCf-4/9. A polymerase chain reaction (PCR)-based procedure for the rapid identification of recombination events between these two markers was developed. The regions of foreign DNA introgression surroundingCf-4 andCf-9 in near-isogenic lines were delimited.
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Affiliation(s)
- P J Balint-Kurti
- Sainsbury Laboratory, John Innes Centre for Plant Science Research, Colney Lane, NR4 7UH, Norwich, England, UK
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48
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Overduin B, van der Biezen EA, John H, Nijkamp J, Hille J. Isolation of Plant Genes by Transposon Tagging: from Concept to Realization. BIOTECHNOL BIOTEC EQ 1994. [DOI: 10.1080/13102818.1994.10818781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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